LAMMPS (1 Feb 2014)
# SRD diffusion demo - ellipsoids

units		lj
atom_style	ellipsoid
atom_modify	first big
dimension	2

# create big ellipsoidal particles

lattice		sq 0.14
Lattice spacing in x,y,z = 2.67261 2.67261 2.67261
region		box block 0 10 0 10 -0.5 0.5
create_box	2 box
Created orthogonal box = (0 0 -1.33631) to (26.7261 26.7261 1.33631)
  4 by 2 by 1 MPI processor grid
create_atoms	1 region box
Created 100 atoms

set		type 1 mass 1.0
  100 settings made for mass
set		type 1 shape 3.0 1.0 1.0
  100 settings made for shape
group		big type 1
100 atoms in group big
set		group big quat/random 29898
  100 settings made for quat/random

velocity	big create 1.44 87287 loop geom

# equilibrate big particles

pair_style      gayberne 1.0 3.0 1.0 4.0
pair_coeff      1 1 1.0 1.0 1 1 1 1 1 1
pair_coeff      1 2 1.0 1.0 1 1 1 1 1 1 0.0
pair_coeff      2 2 1.0 1.0 1 1 1 1 1 1 0.0

neighbor	0.3 bin
neigh_modify	delay 0 every 1 check yes

fix		1 big nve/asphere
fix		2 all enforce2d

compute		rot big temp/asphere

#dump		1 all custom 10 dump.ellipsoid.equil id type x y z #		  quatw quati quatj quatk

thermo_style	custom step temp c_rot epair etotal press
thermo		100

run		1000
Memory usage per processor = 3.31932 Mbytes
Step Temp rot E_pair TotEng Press 
       0         1.44   0.95677852    2.7038078    4.1294078    10.518912 
     100    2.5524145     2.801098  -0.37027046    2.1566199   0.84703874 
     200    2.6266386    2.7938164  -0.35322565    2.2471465     1.004886 
     300    2.9987557    2.9499545  -0.58917376    2.3795944   0.73081788 
     400    2.8557446    2.8208128  -0.39904801    2.4281391   0.91808964 
     500    2.4399047    2.8255746  -0.40056447    2.0149412    1.0538908 
     600     2.854258    2.9166789  -0.53424483    2.2914706    0.8117508 
     700    2.9593679    2.8231211  -0.40051714    2.5292571    1.1630889 
     800    2.7632971    2.9060854  -0.52075339    2.2149107   0.77106814 
     900    2.9905601    2.8869672  -0.49099457    2.4696599   0.69616725 
    1000    2.8470146    2.9004954  -0.51281252     2.305732   0.68820531 
Loop time of 0.0485955 on 8 procs for 1000 steps with 100 atoms

Pair  time (%) = 0.0201517 (41.4682)
Neigh time (%) = 0.000492364 (1.01319)
Comm  time (%) = 0.0191883 (39.4858)
Outpt time (%) = 0.000273198 (0.562188)
Other time (%) = 0.00848994 (17.4706)

Nlocal:    12.5 ave 16 max 8 min
Histogram: 1 1 0 0 0 3 0 0 1 2
Nghost:    34.125 ave 42 max 28 min
Histogram: 1 0 2 2 0 1 0 1 0 1
Neighs:    46.125 ave 65 max 20 min
Histogram: 1 0 1 0 1 2 0 0 1 2

Total # of neighbors = 369
Ave neighs/atom = 3.69
Neighbor list builds = 174
Dangerous builds = 0

#undump		1
unfix		1
unfix		2

# add small particles as hi density lattice

region		plane block INF INF INF INF -0.001 0.001 units box
lattice		sq 120.0
Lattice spacing in x,y,z = 0.0912871 0.0912871 0.0912871
create_atoms	2 region plane
Created 85849 atoms

set		type 2 mass 0.01
  85849 settings made for mass
group		small type 2
85849 atoms in group small
velocity	small create 1.0 593849 loop geom

# delete overlaps
# must set 1-2 cutoff to non-zero value

pair_style	lj/cut 2.5
pair_coeff	1 1 1.0 1.0
pair_coeff	2 2 0.0 1.0 0.0
pair_coeff	1 2 0.0 1.0 2.0

neigh_modify	one 10000

delete_atoms	overlap 1.6 small big
Deleted 71060 atoms, new total = 14889

# SRD run

reset_timestep	0

neighbor	0.3 bin
neigh_modify	delay 0 every 1 check yes

communicate	multi group big vel yes
neigh_modify	include big

# no pairwise interactions with small particles

pair_style      gayberne 1.0 3.0 1.0 4.0
pair_coeff      1 1 1.0 1.0 1 1 1 1 1 1
pair_coeff      1 2 1.0 1.0 1 1 1 1 1 1 0.0
pair_coeff      2 2 1.0 1.0 1 1 1 1 1 1 0.0

# use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles

timestep	0.0005

fix		1 big nve/asphere
fix	        2 small srd 20 big 1.0 0.25 49894 shift yes 54979 		  collision noslip search 0.2 inside ignore exact no bounce 50
fix		3 all enforce2d

# diagnostics

compute		tbig big temp/asphere
variable	pebig equal pe*atoms/count(big)
variable	ebig equal etotal*atoms/count(big)
thermo_style	custom step temp c_rot f_2[9] etotal v_pebig v_ebig press 		f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] 		f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]

thermo_modify	temp tbig
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
thermo		1000

#dump		1 all custom 1000 dump.ellipsoid id type x y z #                quatw quati quatj quatk

#dump		1 all image 1000 image.*.jpg type type zoom 1.6
#dump_modify	1 pad 6 adiam 1 1 adiam 2 0.2

run		100000
SRD info:
  SRD/big particles = 14789 100
  big particle diameter max/min = 3 1
  SRD temperature & lamda = 1 0.1
  SRD max distance & max velocity = 0.4 40
  SRD grid counts: 107 107 1
  SRD grid size: request, actual (xyz) = 0.25, 0.249777 0.249777 2.67261
  SRD per actual grid cell = 1.92757
  SRD viscosity = 0.688101
  big/SRD mass density ratio = 1.37367
  # of rescaled SRD velocities = 0
  ave/max small velocity = 13.3093 24.3359
  ave/max big velocity = 2.08028 5.05671
Memory usage per processor = 10.9077 Mbytes
Step Temp rot 2[9] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[7] 2[8] 2[9] 2[10] 2[11] 2[12] 
       0    2.9004954    2.9004954            0  0.025582146  -0.51281252    3.8089257   0.89865242            0            0            0            0            0            0            0            0            0            0            0            0 
    1000    3.3106106    3.3106106    1.0635866  0.029956176  -0.47263474    4.4601751    1.8111247        14000           35          160            0       224946        98040        11449         4182    1.0635866         1047           50            0 
    2000    2.2814487    2.2814487    1.2237286  0.017972589  -0.72341981    2.6759388    1.3454977        15318           47          276            0       528340        98040        11449         4136    1.2237286         2383           50            0 
    3000    4.2476485    4.2476485    1.2992612  0.038526442  -0.59279435    5.7362019    1.6896403        16506           63          410            0       830594        98040        11449         4172    1.2992612         3834           50            0 
    4000    2.4798681    2.4798681    1.3453264  0.022837826  -0.29467953    3.4003239    2.0765724        17201           51          403            0      1185573        98040        11449         4233    1.3453264         5456           50            0 
    5000    3.0852629    3.0852629    1.3915904   0.02760985  -0.48621111    4.1108305    1.2676357        17540           61          591            0      1594856        98040        11449         4306    1.3915904         7419           50            0 
    6000    6.7201122    6.7201122    1.3649223  0.064627842  -0.39052776    9.6224394    2.5524159        17997           59          564            0      2010250        98040        11449         4213    1.3649223         9280           50            0 
    7000     2.720343     2.720343    1.3909677  0.024282471  -0.43789405    3.6154171    1.5288376        17922           64          342            0      2392388        98040        11449         4228    1.3909677        10947           50            0 
    8000    1.9181626    1.9181626    1.3514483  0.014305579  -0.72810462    2.1299577   0.89423917        18188           42          260            0      2751626        98040        11449         4236    1.3514483        12556           50            0 
    9000    2.9090186    2.9090186    1.3688847   0.02558926  -0.52445278    3.8099849    1.1756318        18536           63          440            0      3112508        98040        11449         4227    1.3688847        14164           50            0 
   10000    1.9647403    1.9647403    1.3979066  0.015375037  -0.63827389    2.2891892   0.65597214        18817           60          466            0      3501352        98040        11449         4257    1.3979066        16016           50            0 
   11000    1.9989051    1.9989051    1.3872043  0.016191243  -0.56765443    2.4107142   0.80582429        18756           58          767            0      3856028        98040        11449         4254    1.3872043        17611           50            0 
   12000    1.7538755    1.7538755    1.4594883  0.013930543  -0.53915598    2.0741185    1.0563875        18602           58          335            0      4248666        98040        11449         4251    1.4594883        19350           50            0 
   13000    13.730871    13.730871    1.4864545   0.13447802  -0.43656501    20.022433    3.6701166        19144           74          681            0      4708523        98040        11449         4104    1.4864545        21589           50            0 
   14000    5.1078782    5.1078782    1.3637807  0.049721182  -0.20775172    7.4029868     2.559935        18494           65          713            0      5139143        98040        11449         4167    1.3637807        23555           50            0 
   15000    2.5843962    2.5843962    1.3450247  0.022294373  -0.53134114    3.3194092    1.1069147        18489           52          260            0      5489252        98040        11449         4262    1.3450247        25209           50            0 
ERROR: Lost atoms: original 14889 current 14819 (../thermo.cpp:392)
